[gmx-users] Truncated Octahedron Box

Chng Choon Peng cpchng at bii.a-star.edu.sg
Tue Jun 1 02:48:47 CEST 2004

Hi Seonah,

  More precisely, it's:
-pbc whole -ur compact
(option whole lets you see whole molecules; '-ur' for setting unit cell
representation to compact which is good for visualizing truncated
octahedrons, the shape I use too)


Mr. Choon-Peng CHNG
Research Associate
Computational Biology Group
BioInformatics Institute, BMSI, A*STAR
30 Biopolis Street
#07-01 Matrix Building
Singapore 138671
Tel (O): +65 64788301 Fax (O): +65 64789047

On 6/1/04 4:05 AM, "David" <spoel at xray.bmc.uu.se> wrote:

> On Mon, 2004-05-31 at 19:06, Seonah Kim wrote:
>> Hello All,
>> I asked Villin Benchmark for octahedron box and Dr. Spoel replied to me that
>> if 
>> I use trjconv command, I can see the octahedron box.
>> I still have one more question about trjconv.
>> I used trjconv option like,
>>> trjconv -f full.trr -s full.tpr -o full.pdb
> add -pbc compact (or something like that)
>> Now, I got the full.pdb file and upload this pdb file using VMD but it still
>> looks like cubic box instead of octahedron box. Did I miss something to see
>> octahedron box? If someone knows this solution, I'll greatly happy for this.
>> :)
>> Thank you for your help in advance...
>> Seonah Kim
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